5  Archaeobotany

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The results presented here are preliminary and the chapter has yet to be written.

In this chapter, I will present the macrobotanical data from X case studies used to carry on this research [reference to the Materials chapter], along with the quantifications performed on the absolute counts. The data will be first presented temporally, and a discussion of the diachronic trends will follow at the end of the chapter.

5.1 Case studies

The following map shows the sites under investigation, divided by chronology. Please select the desired chronology (or chronologies) from the legend on the right.

5.2 Ubiquity

In Chapter 4 ubiquity has been described as the best way to present the archaeobotanical remains from the Italian peninsula, given the numerous biases in the samples. The heatmap below (Figure 5.1) provides a good overview of the temporal trends of presence of cereals, legumes, fruits and nuts in the entire area under examination.

Show the code

# Load the libraries
# Note: these libraries are used for the data visualizations in this page.
library(RColorBrewer)
library(reshape2)
library(ggplot2)
library(hrbrthemes)
library(plotly)
library(patchwork)

## UBIQUITY

## Creating a dataframe that contains the ubiquity of each century under examination. 
Ubiquity_table <- data.frame(
  "I BCE" = archaeobotany_tables(plants_export, -1)$Ubiquity_exp,  
  "I CE" = archaeobotany_tables(plants_export, 1)$Ubiquity_exp,
  "II CE" = archaeobotany_tables(plants_export, 2)$Ubiquity_exp,
  "III CE" = archaeobotany_tables(plants_export, 3)$Ubiquity_exp,
  "IV CE" = archaeobotany_tables(plants_export, 4)$Ubiquity_exp,
  "V CE" = archaeobotany_tables(plants_export, 5)$Ubiquity_exp,
  "VI CE" = archaeobotany_tables(plants_export, 6)$Ubiquity_exp,
  "VII CE" = archaeobotany_tables(plants_export, 7)$Ubiquity_exp,
  "VIII CE" = archaeobotany_tables(plants_export, 8)$Ubiquity_exp,
  "IX CE" = archaeobotany_tables(plants_export, 9)$Ubiquity_exp,
  "X CE" = archaeobotany_tables(plants_export, 10)$Ubiquity_exp,
  "XI CE" = archaeobotany_tables(plants_export, 11)$Ubiquity_exp
  )

# Transform the ubiquity table into a matrix
Ubiquity_mat <- as.matrix(Ubiquity_table) 

# Rename the centuries
colnames(Ubiquity_mat) <- c("1st c. BCE", "1st c. CE", "2nd c. CE",
                            "3rd c. CE", "4th c. CE", "5th c. CE",
                            "6th c. CE", "7th c. CE", "8th c. CE",
                            "9th c. CE", "10th c. CE", "11th c. CE") 

# The data has to be molten to use it with ggplot2
# (package: reshape2)
Ubiquity_melt <- melt(Ubiquity_mat)

# Let's now rename the columns 
colnames(Ubiquity_melt) <- c("Taxon", "Century", "Ubiquity")

# Add a column for the text tooltip
Ubiquity_melt <- Ubiquity_melt %>%
  mutate(text = paste0("Taxon: ", Taxon, "\n", "Century: ", Century, "\n", "Value: ",round(Ubiquity,2)))

# Create the heatmap with ggplot2
Ubiquity_HM <- ggplot(Ubiquity_melt, aes(Century, Taxon, fill=Ubiquity, text=text)) + 
  geom_tile(colour="white") +
  scale_alpha(range=c(0,1)) +
  scale_x_discrete("", expand = c(0, 0)) + 
  scale_y_discrete("", expand = c(0, 0)) + 
  theme_grey(base_size = 9) + 
  theme(legend.position = "right",
        axis.ticks = element_blank(), 
        axis.text.x = element_text(angle = 90, hjust = 0)
        ) +
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())+
  labs(
    title="Ubiquity",
    subtitle="Diachronical heatmap of recorded plant species"
  ) +
  scale_fill_gradient(low = "white", high = "black")

Figure 5.1: Diachronical heatmap of recorded plant species